Controlling protein molecular dynamics:how to accelerate folding while preserving the native state

The dynamics of peptides and proteins generated by classical molecular dynamics (MD) is described by using a Markov model. The model is built by clustering the trajectory into conformational states and estimating transition probabilities between the states. Assuming that it is possible to influence the dynamics of the system by varying simulation parameters, we show how to use the Markov model to determine the parameter values that preserve the folded state of the protein and at the same time, reduce the folding time in the simulation. We investigate this by applying the method to two systems. The first system is an imaginary peptide described by given transition probabilities with a total folding time of 1 micros. We find that only small changes in the transition probabilities are needed to accelerate (or decelerate) the folding. This implies that folding times for slowly folding peptides and proteins calculated using MD cannot be meaningfully compared to experimental results. The second system is a four residue peptide valine-proline-alanine-leucine in water. We control the dynamics of the transitions by varying the temperature and the atom masses. The simulation results show that it is possible to find the combinations of parameter values that accelerate the dynamics and at the same time preserve the native state of the peptide. A method for accelerating larger systems without performing simulations for the whole folding process is outlined.

Clustering epileptiform discharges in the interictal electroencephalogram with topography preserving maps

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Making memories available:a framework for preserving rural heritage through community knowledge management (cKM)

While most of the research in Knowledge Management (KM) has focused on business communities, there is a breadth of potential applications of KM theory and practice to wider society. This paper explores the potential of KM for rural communities, specifically for those that want to preserve their social history and collective memories (what we call heritage) to enrich the lives of others. In KM terms, this is a task of accumulating and recording knowledge (using KM techniques such as story-telling and communities of practice) to enable its retention for future use (by interested people perhaps through KM systems). We report a case study of Cardrona, a valley of approximately 120 people in New Zealand's South Island. Realising that time would erode knowledge of their community a small, motivated group of residents initiated a KM programme to create a legacy for a wider community including younger generations, tourists and scholars. This paper applies KM principles to rural communities that want to harness their collective knowledge for wider societal gain, and develops a community-based framework to inform such initiatives. As a result, we call for a wider conceptualisation of KM to include motives for managing knowledge beyond business performance to accommodate community (cKM). © 2010 Operational Research Society.

On the sense preserving mappings in the Helm topology in the plane

∗Research supported by the grant No. GAUK 186/96 of Charles University.

The Role of the National Library in Preserving National Written Heritage

The first part presented at the meeting by A. Dipchikova is a brief report of the role of the National library as an institution in collecting, preserving and making accessible the national written heritage. Problems of digitization are examined from the point of view of the existing experience in cataloguing. Special attention is paid to the history and the significance of international standards, the experience in the field of development and maintenance of authority files on national and international level as well as in markup languages. Possibilities of using MARC and XML in the library are discussed. The second part presented here by E. Moussakova is giving an overview of the latest activities of the Library in the sphere of digitisation of the old Slavic manuscripts which are component of the national cultural heritage. It is pointed out that the current work is rather limited within the scope of preparation of metadata than being focused on digital products.

On a Convexity Preserving Integral Operator

MSC 2010: 30C45, 30A20, 34C40

Classification of the Maximal Subsemigroups of the Semigroup of all Partial Order-Preserving Transformations

Илинка А. Димитрова, Цветелина Н. Младенова - Моноида P Tn от всички частични преобразования върху едно n-елементно множество относно операцията композиция на преобразования е изучаван в различни аспекти от редица автори. Едно частично преобразование α се нарича запазващо наредбата, ако от x ≤ y следва, че xα ≤ yα за всяко x, y от дефиниционното множество на α. Обект на разглеждане в настоящата работа е моноида P On състоящ се от всички частични запазващи наредбата преобразования. Очевидно P On е под-моноид на P Tn. Направена е пълна класификация на максималните подполугрупи на моноида P On. Доказано е, че съществуват пет различни вида максимални подполугрупи на разглеждания моноид. Броят на всички максимални подполугрупи на POn е точно 2^n + 2n − 2.

Preserving Cultural Heritage Using Open Source Collection Management Tools

Open source software (OSS) popularity is growing steadily and many OSS systems could be used to preserve cultural heritage objects. Such solutions give the opportunity to organizations to afford the development of a digital collection. This paper focuses on reviewing two OSS tools, CollectionSpace and the Open Video Digital Library Toolkit and discuss on how these could be used for organizing digital replicas of cultural objects. The features of the software are presented and some examples are given.

Preserving Linked Data

PRELIDA (PREserving LInked DAta) is an FP7 Coordination Action funded by the European Commission under the Digital Preservation Theme. PRELIDA targets the particular stakeholders of the Linked Data community, including data providers, service providers, technology providers and end user communities. These stakeholders have not been traditionally targeted by the Digital Preservation community, and are typically not aware of the digital preservation solutions already available. So an important task of PRELIDA is to raise awareness of existing preservation solutions and to facilitate their uptake. At the same time, the Linked Data cloud has specific characteristics in terms of structuring, interlinkage, dynamicity and distribution that pose new challenges to the preservation community. PRELIDA organises in-depth discussions among the two communities to identify which of these characteristics require novel solutions, and to develop road maps for addressing the new challenges. PRELIDA will complete its lifecycle at the end of this year, and the talk will report about the major findings.

PanamaTipico.com: a Born Digital Initiative for Researching and Preserving Panama’s Cultural Heritage

This paper reflects on the experience of PanamaTipico.com, an independent website specialized in the research and preservation of the cultural heritage of the Republic of Panama, a developing country located in Central America. Basic information about the project is described. Also discussed, are some of the challenges confronted by the project and the results achieved. The goal of this paper is to encourage a discussion on whether or not the experience of Pan-amaTipico.com is comparable to the experiences of similar projects in developing countries in Eastern Europe and elsewhere.

Case-based reasoning enabling database mining for cryo-preserving algae applications

Case-based Reasoning's (CBR) origins were stimulated by a desire to understand how people remember information and are in turn reminded of information, and that subsequently it was recognized that people commonly solve problems by remembering how they solved similar problems in the past. Thus CBR became an appropriate way to find out the most suitable solution method for a new problem based on the old methods for the same or even similar problems. The research highlights how to use CBR to aid biologists in finding the best method to cryo preserve algae. The study found CBR could be used successfully to find the similarity percentage between the new algae and old cases in the case base. The prediction result showed approximately 93.75% accuracy, which proves the CBR system can offer appropriate recommendations for most situations. © 2011 IEEE.